+Open data
-Basic information
Entry | Database: PDB / ID: 6yn7 | ||||||
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Title | Crystal Structure of AHE enzyme from Alicyclobacillus herbarius | ||||||
Components | AHE, beta-glucosidase enzyme | ||||||
Keywords | HYDROLASE / AHE / Alicyclobacillus herbarius / beta-glucosidase | ||||||
Function / homology | NICKEL (II) ION / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL Function and homology information | ||||||
Biological species | Alicyclobacillus herbarius (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å | ||||||
Authors | Gourlay, L.J. / Di Pisa, F. | ||||||
Citation | Journal: Chembiochem / Year: 2021 Title: Release of Soybean Isoflavones by Using a beta-Glucosidase from Alicyclobacillus herbarius. Authors: Delgado, L. / Heckmann, C.M. / Di Pisa, F. / Gourlay, L. / Paradisi, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yn7.cif.gz | 449.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yn7.ent.gz | 295.5 KB | Display | PDB format |
PDBx/mmJSON format | 6yn7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6yn7_validation.pdf.gz | 7.9 MB | Display | wwPDB validaton report |
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Full document | 6yn7_full_validation.pdf.gz | 7.9 MB | Display | |
Data in XML | 6yn7_validation.xml.gz | 63 KB | Display | |
Data in CIF | 6yn7_validation.cif.gz | 86.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yn/6yn7 ftp://data.pdbj.org/pub/pdb/validation_reports/yn/6yn7 | HTTPS FTP |
-Related structure data
Related structure data | 4ptvS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 51601.305 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alicyclobacillus herbarius (bacteria) / Production host: Escherichia coli (E. coli) / References: beta-galactosidase |
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-Non-polymers , 5 types, 304 molecules
#2: Chemical | ChemComp-EDO / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-PEG / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.3 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.2 M NaBr, 20% w/v PEG 3350 0.1 M BT Propane, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 19, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.976→105.161 Å / Num. obs: 58817 / % possible obs: 93.5 % / Redundancy: 6.8 % / Biso Wilson estimate: 23.88 Å2 / CC1/2: 0.996 / Net I/σ(I): 7 |
Reflection shell | Resolution: 1.976→2.267 Å / Num. unique obs: 2941 / CC1/2: 0.693 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4PTV Resolution: 1.98→98.9 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 41.3199
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.62 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.98→98.9 Å
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Refine LS restraints |
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LS refinement shell |
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